Starting phenix.real_space_refine on Thu May 29 10:25:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ss2_40741/05_2025/8ss2_40741.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ss2_40741/05_2025/8ss2_40741.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ss2_40741/05_2025/8ss2_40741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ss2_40741/05_2025/8ss2_40741.map" model { file = "/net/cci-nas-00/data/ceres_data/8ss2_40741/05_2025/8ss2_40741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ss2_40741/05_2025/8ss2_40741.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 20 5.49 5 S 166 5.16 5 C 20273 2.51 5 N 4965 2.21 5 O 5710 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 31146 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7714 Classifications: {'peptide': 978} Link IDs: {'PCIS': 3, 'PTRANS': 24, 'TRANS': 950} Chain breaks: 4 Chain: "B" Number of atoms: 6177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6177 Classifications: {'peptide': 783} Link IDs: {'PCIS': 4, 'PTRANS': 19, 'TRANS': 759} Chain breaks: 2 Chain: "C" Number of atoms: 7714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7714 Classifications: {'peptide': 978} Link IDs: {'PCIS': 3, 'PTRANS': 24, 'TRANS': 950} Chain breaks: 4 Chain: "D" Number of atoms: 6177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6177 Classifications: {'peptide': 783} Link IDs: {'PCIS': 4, 'PTRANS': 19, 'TRANS': 759} Chain breaks: 2 Chain: "E" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1166 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Chain: "F" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1166 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Chain: "A" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 313 Unusual residues: {'AJP': 1, 'CLR': 1, 'PCW': 7, 'SPD': 1, 'ZK1': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 270 Unresolved non-hydrogen dihedrals: 263 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'PCW:plan-1': 3, 'PCW:plan-2': 3, 'PCW:plan-3': 3, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 154 Unusual residues: {'PCW': 4, 'ZK1': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 2, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 303 Unusual residues: {'AJP': 1, 'CLR': 1, 'PCW': 7, 'ZK1': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 270 Unresolved non-hydrogen dihedrals: 263 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'PCW:plan-1': 3, 'PCW:plan-2': 3, 'PCW:plan-3': 3, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 43 Chain: "D" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 154 Unusual residues: {'PCW': 4, 'ZK1': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 2, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'PCW': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'PCW': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 16.29, per 1000 atoms: 0.52 Number of scatterers: 31146 At special positions: 0 Unit cell: (117.03, 163.51, 197.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 166 16.00 P 20 15.00 F 12 9.00 O 5710 8.00 N 4965 7.00 C 20273 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 315 " distance=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.04 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 900 " distance=2.04 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.00 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.06 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.04 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 900 " distance=2.04 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.00 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.08 Conformation dependent library (CDL) restraints added in 4.0 seconds 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7020 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 38 sheets defined 46.7% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.65 Creating SS restraints... Processing helix chain 'A' and resid 22 through 34 removed outlier: 3.562A pdb=" N MET A 33 " --> pdb=" O PHE A 29 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A 34 " --> pdb=" O ARG A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 67 Processing helix chain 'A' and resid 81 through 92 removed outlier: 3.582A pdb=" N SER A 87 " --> pdb=" O ASN A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 129 removed outlier: 3.788A pdb=" N LEU A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 156 removed outlier: 4.082A pdb=" N ALA A 153 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS A 156 " --> pdb=" O SER A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 181 removed outlier: 3.926A pdb=" N TYR A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ARG A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 186 Processing helix chain 'A' and resid 197 through 211 removed outlier: 3.736A pdb=" N ASP A 203 " --> pdb=" O ASP A 199 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 removed outlier: 3.617A pdb=" N GLY A 230 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ASP A 231 " --> pdb=" O THR A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 237 removed outlier: 4.511A pdb=" N PHE A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 264 removed outlier: 3.625A pdb=" N GLU A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 300 removed outlier: 3.528A pdb=" N ASP A 287 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 289 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A 300 " --> pdb=" O PHE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 removed outlier: 3.595A pdb=" N ASN A 311 " --> pdb=" O ARG A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 335 Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 423 through 436 removed outlier: 3.529A pdb=" N ASP A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 466 Processing helix chain 'A' and resid 522 through 544 removed outlier: 3.659A pdb=" N CYS A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 585 removed outlier: 3.881A pdb=" N MET A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 615 removed outlier: 3.642A pdb=" N TRP A 606 " --> pdb=" O GLY A 602 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 624 removed outlier: 4.673A pdb=" N ALA A 622 " --> pdb=" O ALA A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 641 Processing helix chain 'A' and resid 653 through 661 removed outlier: 3.586A pdb=" N GLU A 657 " --> pdb=" O GLY A 653 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 676 removed outlier: 3.973A pdb=" N LYS A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET A 674 " --> pdb=" O MET A 670 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER A 676 " --> pdb=" O THR A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 696 removed outlier: 3.567A pdb=" N VAL A 693 " --> pdb=" O GLY A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 714 removed outlier: 3.893A pdb=" N TYR A 711 " --> pdb=" O THR A 707 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN A 714 " --> pdb=" O GLU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 748 removed outlier: 3.739A pdb=" N ASN A 747 " --> pdb=" O GLY A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 756 Processing helix chain 'A' and resid 757 through 767 removed outlier: 3.798A pdb=" N LYS A 763 " --> pdb=" O LEU A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 817 removed outlier: 3.534A pdb=" N LEU A 805 " --> pdb=" O GLY A 801 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS A 817 " --> pdb=" O GLU A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 857 removed outlier: 3.788A pdb=" N THR A 838 " --> pdb=" O ARG A 834 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A 857 " --> pdb=" O GLY A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 952 removed outlier: 4.280A pdb=" N LEU A 933 " --> pdb=" O THR A 929 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASN A 947 " --> pdb=" O PHE A 943 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE A 948 " --> pdb=" O ILE A 944 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLY A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N HIS A 950 " --> pdb=" O SER A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 986 removed outlier: 3.823A pdb=" N SER A 962 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE A 965 " --> pdb=" O VAL A 961 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP A 986 " --> pdb=" O SER A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1032 removed outlier: 3.781A pdb=" N LEU A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY A1021 " --> pdb=" O THR A1017 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET A1029 " --> pdb=" O VAL A1025 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 35 removed outlier: 4.324A pdb=" N VAL B 34 " --> pdb=" O ARG B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 68 removed outlier: 3.512A pdb=" N GLN B 65 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG B 68 " --> pdb=" O SER B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 92 removed outlier: 3.929A pdb=" N SER B 87 " --> pdb=" O ASN B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 129 removed outlier: 4.085A pdb=" N LEU B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 150 Processing helix chain 'B' and resid 172 through 187 removed outlier: 3.817A pdb=" N ARG B 178 " --> pdb=" O ASP B 174 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS B 187 " --> pdb=" O ASP B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 210 Processing helix chain 'B' and resid 226 through 230 removed outlier: 4.153A pdb=" N GLY B 230 " --> pdb=" O PHE B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 264 removed outlier: 3.569A pdb=" N SER B 256 " --> pdb=" O ASP B 252 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 300 removed outlier: 3.561A pdb=" N THR B 285 " --> pdb=" O THR B 281 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N PHE B 296 " --> pdb=" O MET B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 334 removed outlier: 4.156A pdb=" N GLU B 330 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA B 332 " --> pdb=" O GLU B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 436 removed outlier: 3.513A pdb=" N ASP B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS B 434 " --> pdb=" O ALA B 430 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N HIS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 469 removed outlier: 3.731A pdb=" N TYR B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 removed outlier: 3.512A pdb=" N GLU B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.838A pdb=" N ASP B 519 " --> pdb=" O SER B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 546 removed outlier: 3.707A pdb=" N VAL B 530 " --> pdb=" O TRP B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.574A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TRP B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 626 removed outlier: 3.633A pdb=" N ILE B 600 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA B 618 " --> pdb=" O SER B 614 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 624 " --> pdb=" O LEU B 620 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR B 625 " --> pdb=" O ALA B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 641 Processing helix chain 'B' and resid 653 through 661 removed outlier: 4.304A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG B 660 " --> pdb=" O LYS B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 677 removed outlier: 3.604A pdb=" N LYS B 669 " --> pdb=" O ALA B 665 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP B 671 " --> pdb=" O PHE B 667 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N MET B 674 " --> pdb=" O MET B 670 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 691 Processing helix chain 'B' and resid 706 through 713 removed outlier: 3.653A pdb=" N GLU B 710 " --> pdb=" O SER B 706 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR B 711 " --> pdb=" O THR B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 756 removed outlier: 3.657A pdb=" N ASN B 747 " --> pdb=" O GLY B 743 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS B 752 " --> pdb=" O LEU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 768 removed outlier: 4.051A pdb=" N LYS B 763 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TRP B 766 " --> pdb=" O LEU B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 817 removed outlier: 3.720A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR B 797 " --> pdb=" O ALA B 793 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA B 806 " --> pdb=" O GLY B 802 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 34 removed outlier: 3.562A pdb=" N MET C 33 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL C 34 " --> pdb=" O ARG C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 67 Processing helix chain 'C' and resid 81 through 92 removed outlier: 3.582A pdb=" N SER C 87 " --> pdb=" O ASN C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 129 removed outlier: 3.789A pdb=" N LEU C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 156 removed outlier: 4.082A pdb=" N ALA C 153 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU C 155 " --> pdb=" O ASP C 151 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS C 156 " --> pdb=" O SER C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 181 removed outlier: 3.926A pdb=" N TYR C 177 " --> pdb=" O LYS C 173 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ARG C 178 " --> pdb=" O ASP C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 186 Processing helix chain 'C' and resid 197 through 211 removed outlier: 3.735A pdb=" N ASP C 203 " --> pdb=" O ASP C 199 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR C 210 " --> pdb=" O ASP C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 231 removed outlier: 3.618A pdb=" N GLY C 230 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ASP C 231 " --> pdb=" O THR C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 237 removed outlier: 4.511A pdb=" N PHE C 237 " --> pdb=" O LEU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 264 removed outlier: 3.625A pdb=" N GLU C 260 " --> pdb=" O SER C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 300 removed outlier: 3.528A pdb=" N ASP C 287 " --> pdb=" O ALA C 283 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL C 289 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL C 291 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG C 300 " --> pdb=" O PHE C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 311 removed outlier: 3.595A pdb=" N ASN C 311 " --> pdb=" O ARG C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 335 Processing helix chain 'C' and resid 417 through 421 Processing helix chain 'C' and resid 423 through 436 removed outlier: 3.530A pdb=" N ASP C 427 " --> pdb=" O GLY C 423 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N HIS C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 466 Processing helix chain 'C' and resid 522 through 544 removed outlier: 3.660A pdb=" N CYS C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL C 539 " --> pdb=" O GLY C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 585 removed outlier: 3.881A pdb=" N MET C 585 " --> pdb=" O LEU C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 615 removed outlier: 3.642A pdb=" N TRP C 606 " --> pdb=" O GLY C 602 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE C 613 " --> pdb=" O THR C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 624 removed outlier: 4.674A pdb=" N ALA C 622 " --> pdb=" O ALA C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 641 Processing helix chain 'C' and resid 653 through 661 removed outlier: 3.586A pdb=" N GLU C 657 " --> pdb=" O GLY C 653 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE C 659 " --> pdb=" O THR C 655 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG C 661 " --> pdb=" O GLU C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 676 removed outlier: 3.973A pdb=" N LYS C 669 " --> pdb=" O ALA C 665 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET C 674 " --> pdb=" O MET C 670 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER C 676 " --> pdb=" O THR C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 696 removed outlier: 3.567A pdb=" N VAL C 693 " --> pdb=" O GLY C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 714 removed outlier: 3.893A pdb=" N TYR C 711 " --> pdb=" O THR C 707 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN C 714 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 748 removed outlier: 3.739A pdb=" N ASN C 747 " --> pdb=" O GLY C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 751 through 756 Processing helix chain 'C' and resid 757 through 767 removed outlier: 3.799A pdb=" N LYS C 763 " --> pdb=" O LEU C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 817 removed outlier: 3.534A pdb=" N LEU C 805 " --> pdb=" O GLY C 801 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS C 817 " --> pdb=" O GLU C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 857 removed outlier: 3.788A pdb=" N THR C 838 " --> pdb=" O ARG C 834 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER C 842 " --> pdb=" O THR C 838 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER C 857 " --> pdb=" O GLY C 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 929 through 952 removed outlier: 4.281A pdb=" N LEU C 933 " --> pdb=" O THR C 929 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN C 947 " --> pdb=" O PHE C 943 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE C 948 " --> pdb=" O ILE C 944 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N HIS C 950 " --> pdb=" O SER C 946 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 986 removed outlier: 3.823A pdb=" N SER C 962 " --> pdb=" O LEU C 958 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE C 965 " --> pdb=" O VAL C 961 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY C 970 " --> pdb=" O PHE C 966 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP C 986 " --> pdb=" O SER C 982 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1032 removed outlier: 3.781A pdb=" N LEU C1015 " --> pdb=" O ALA C1011 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY C1021 " --> pdb=" O THR C1017 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET C1029 " --> pdb=" O VAL C1025 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 35 removed outlier: 4.323A pdb=" N VAL D 34 " --> pdb=" O ARG D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 68 removed outlier: 3.511A pdb=" N GLN D 65 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG D 68 " --> pdb=" O SER D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 92 removed outlier: 3.929A pdb=" N SER D 87 " --> pdb=" O ASN D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 129 removed outlier: 4.086A pdb=" N LEU D 122 " --> pdb=" O LYS D 118 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 150 Processing helix chain 'D' and resid 172 through 187 removed outlier: 3.818A pdb=" N ARG D 178 " --> pdb=" O ASP D 174 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS D 187 " --> pdb=" O ASP D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 210 Processing helix chain 'D' and resid 226 through 230 removed outlier: 4.154A pdb=" N GLY D 230 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 264 removed outlier: 3.569A pdb=" N SER D 256 " --> pdb=" O ASP D 252 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG D 261 " --> pdb=" O LYS D 257 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 300 removed outlier: 3.562A pdb=" N THR D 285 " --> pdb=" O THR D 281 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N PHE D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 334 removed outlier: 4.156A pdb=" N GLU D 330 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA D 332 " --> pdb=" O GLU D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 436 removed outlier: 3.513A pdb=" N ASP D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS D 434 " --> pdb=" O ALA D 430 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N HIS D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 469 removed outlier: 3.731A pdb=" N TYR D 469 " --> pdb=" O GLY D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 487 removed outlier: 3.513A pdb=" N GLU D 487 " --> pdb=" O LEU D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.839A pdb=" N ASP D 519 " --> pdb=" O SER D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 546 removed outlier: 3.707A pdb=" N VAL D 530 " --> pdb=" O TRP D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 removed outlier: 3.575A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 626 removed outlier: 3.633A pdb=" N ILE D 600 " --> pdb=" O LEU D 596 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP D 606 " --> pdb=" O GLY D 602 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER D 614 " --> pdb=" O LEU D 610 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA D 618 " --> pdb=" O SER D 614 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU D 624 " --> pdb=" O LEU D 620 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR D 625 " --> pdb=" O ALA D 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 641 Processing helix chain 'D' and resid 653 through 661 removed outlier: 4.304A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG D 660 " --> pdb=" O LYS D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 677 removed outlier: 3.603A pdb=" N LYS D 669 " --> pdb=" O ALA D 665 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP D 671 " --> pdb=" O PHE D 667 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N MET D 674 " --> pdb=" O MET D 670 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 691 Processing helix chain 'D' and resid 706 through 713 removed outlier: 3.652A pdb=" N GLU D 710 " --> pdb=" O SER D 706 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR D 711 " --> pdb=" O THR D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 756 removed outlier: 3.657A pdb=" N ASN D 747 " --> pdb=" O GLY D 743 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS D 752 " --> pdb=" O LEU D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 768 removed outlier: 4.051A pdb=" N LYS D 763 " --> pdb=" O LEU D 759 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TRP D 766 " --> pdb=" O LEU D 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 817 removed outlier: 3.721A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR D 797 " --> pdb=" O ALA D 793 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA D 806 " --> pdb=" O GLY D 802 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 18 removed outlier: 3.661A pdb=" N MET E 11 " --> pdb=" O ALA E 7 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL E 15 " --> pdb=" O MET E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 36 removed outlier: 3.539A pdb=" N ALA E 30 " --> pdb=" O TRP E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 67 removed outlier: 3.529A pdb=" N LEU E 64 " --> pdb=" O ILE E 60 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS E 66 " --> pdb=" O CYS E 62 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 85 removed outlier: 3.733A pdb=" N GLU E 71 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N HIS E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU E 80 " --> pdb=" O GLY E 76 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU E 83 " --> pdb=" O CYS E 79 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS E 84 " --> pdb=" O LEU E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 105 Proline residue: E 96 - end of helix removed outlier: 3.655A pdb=" N TYR E 100 " --> pdb=" O PRO E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 158 removed outlier: 3.811A pdb=" N GLU E 134 " --> pdb=" O TYR E 130 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TRP E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS E 138 " --> pdb=" O GLU E 134 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU E 150 " --> pdb=" O PHE E 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 18 removed outlier: 3.661A pdb=" N MET F 11 " --> pdb=" O ALA F 7 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL F 15 " --> pdb=" O MET F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 36 removed outlier: 3.540A pdb=" N ALA F 30 " --> pdb=" O TRP F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 67 removed outlier: 3.529A pdb=" N LEU F 64 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS F 66 " --> pdb=" O CYS F 62 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU F 67 " --> pdb=" O LEU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 85 removed outlier: 3.734A pdb=" N GLU F 71 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N HIS F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU F 80 " --> pdb=" O GLY F 76 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU F 83 " --> pdb=" O CYS F 79 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS F 84 " --> pdb=" O LEU F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 105 Proline residue: F 96 - end of helix removed outlier: 3.654A pdb=" N TYR F 100 " --> pdb=" O PRO F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 158 removed outlier: 3.812A pdb=" N GLU F 134 " --> pdb=" O TYR F 130 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP F 136 " --> pdb=" O GLN F 132 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS F 138 " --> pdb=" O GLU F 134 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU F 139 " --> pdb=" O SER F 135 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE F 147 " --> pdb=" O LEU F 143 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU F 150 " --> pdb=" O PHE F 146 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 47 removed outlier: 3.770A pdb=" N ILE A 12 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS A 46 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 10.082A pdb=" N ALA A 72 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N GLN A 13 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N PHE A 74 " --> pdb=" O GLN A 13 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N GLY A 15 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ILE A 73 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE A 96 " --> pdb=" O ILE A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 243 through 246 removed outlier: 3.650A pdb=" N GLY A 244 " --> pdb=" O MET A 361 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET A 361 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY A 367 " --> pdb=" O LYS A 364 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 339 through 340 Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 374 Processing sheet with id=AA5, first strand: chain 'A' and resid 398 through 399 Processing sheet with id=AA6, first strand: chain 'A' and resid 479 through 480 removed outlier: 4.096A pdb=" N LEU A 479 " --> pdb=" O GLY A 733 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 490 through 491 Processing sheet with id=AA8, first strand: chain 'A' and resid 703 through 705 removed outlier: 4.143A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 649 through 650 removed outlier: 5.961A pdb=" N THR A 649 " --> pdb=" O VAL A 683 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 876 through 878 Processing sheet with id=AB2, first strand: chain 'A' and resid 889 through 890 Processing sheet with id=AB3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.771A pdb=" N PHE B 96 " --> pdb=" O ILE B 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 220 through 221 removed outlier: 6.607A pdb=" N TYR B 220 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N PHE B 245 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET B 361 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY B 372 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B 375 " --> pdb=" O LYS B 379 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LYS B 379 " --> pdb=" O SER B 375 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 338 through 340 removed outlier: 3.560A pdb=" N VAL B 338 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 395 through 399 removed outlier: 3.535A pdb=" N VAL B 397 " --> pdb=" O LYS B 441 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB8, first strand: chain 'B' and resid 479 through 480 removed outlier: 4.340A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AC1, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.827A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL B 723 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 42 through 47 removed outlier: 3.770A pdb=" N ILE C 12 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS C 46 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 10.082A pdb=" N ALA C 72 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N GLN C 13 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N PHE C 74 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N GLY C 15 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ILE C 73 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE C 96 " --> pdb=" O ILE C 111 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 243 through 246 removed outlier: 3.651A pdb=" N GLY C 244 " --> pdb=" O MET C 361 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET C 361 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY C 367 " --> pdb=" O LYS C 364 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 339 through 340 Processing sheet with id=AC5, first strand: chain 'C' and resid 372 through 374 Processing sheet with id=AC6, first strand: chain 'C' and resid 398 through 399 Processing sheet with id=AC7, first strand: chain 'C' and resid 479 through 480 removed outlier: 4.096A pdb=" N LEU C 479 " --> pdb=" O GLY C 733 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 490 through 491 Processing sheet with id=AC9, first strand: chain 'C' and resid 703 through 705 removed outlier: 4.143A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 649 through 650 removed outlier: 5.962A pdb=" N THR C 649 " --> pdb=" O VAL C 683 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 876 through 878 Processing sheet with id=AD3, first strand: chain 'C' and resid 889 through 890 Processing sheet with id=AD4, first strand: chain 'D' and resid 96 through 98 removed outlier: 6.770A pdb=" N PHE D 96 " --> pdb=" O ILE D 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 220 through 221 removed outlier: 6.608A pdb=" N TYR D 220 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N PHE D 245 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET D 361 " --> pdb=" O GLY D 244 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY D 372 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER D 375 " --> pdb=" O LYS D 379 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LYS D 379 " --> pdb=" O SER D 375 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 338 through 340 removed outlier: 3.560A pdb=" N VAL D 338 " --> pdb=" O ILE D 345 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE D 345 " --> pdb=" O VAL D 338 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 395 through 399 removed outlier: 3.534A pdb=" N VAL D 397 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AD9, first strand: chain 'D' and resid 479 through 480 removed outlier: 4.340A pdb=" N LEU D 479 " --> pdb=" O GLY D 733 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AE2, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.827A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL D 723 " --> pdb=" O ILE D 502 " (cutoff:3.500A) 1093 hydrogen bonds defined for protein. 3201 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.38 Time building geometry restraints manager: 9.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.08 - 0.51: 4 0.51 - 0.94: 0 0.94 - 1.36: 10295 1.36 - 1.79: 21401 1.79 - 2.22: 113 Warning: very small bond lengths. Bond restraints: 31813 Sorted by residual: bond pdb=" C27 AJP C1106 " pdb=" O78 AJP C1106 " ideal model delta sigma weight residual 1.406 0.083 1.323 2.00e-02 2.50e+03 4.38e+03 bond pdb=" C27 AJP A1106 " pdb=" O78 AJP A1106 " ideal model delta sigma weight residual 1.406 0.151 1.255 2.00e-02 2.50e+03 3.94e+03 bond pdb=" C23 AJP A1106 " pdb=" O25 AJP A1106 " ideal model delta sigma weight residual 1.423 0.491 0.932 2.00e-02 2.50e+03 2.17e+03 bond pdb=" C23 AJP C1106 " pdb=" O25 AJP C1106 " ideal model delta sigma weight residual 1.423 0.495 0.928 2.00e-02 2.50e+03 2.15e+03 bond pdb=" C26 AJP C1106 " pdb=" O25 AJP C1106 " ideal model delta sigma weight residual 1.375 2.069 -0.694 2.00e-02 2.50e+03 1.21e+03 ... (remaining 31808 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.37: 41816 4.37 - 8.75: 948 8.75 - 13.12: 138 13.12 - 17.49: 12 17.49 - 21.87: 6 Bond angle restraints: 42920 Sorted by residual: angle pdb=" C ALA A 317 " pdb=" N ASN A 318 " pdb=" CA ASN A 318 " ideal model delta sigma weight residual 120.51 132.81 -12.30 1.45e+00 4.76e-01 7.20e+01 angle pdb=" C ALA C 317 " pdb=" N ASN C 318 " pdb=" CA ASN C 318 " ideal model delta sigma weight residual 120.51 132.75 -12.24 1.45e+00 4.76e-01 7.13e+01 angle pdb=" C17 CLR A1105 " pdb=" C13 CLR A1105 " pdb=" C18 CLR A1105 " ideal model delta sigma weight residual 110.18 88.31 21.87 3.00e+00 1.11e-01 5.31e+01 angle pdb=" C28 AJP A1106 " pdb=" C27 AJP A1106 " pdb=" O78 AJP A1106 " ideal model delta sigma weight residual 108.61 129.29 -20.68 3.00e+00 1.11e-01 4.75e+01 angle pdb=" C04 AJP A1106 " pdb=" C05 AJP A1106 " pdb=" C06 AJP A1106 " ideal model delta sigma weight residual 114.54 134.46 -19.92 3.00e+00 1.11e-01 4.41e+01 ... (remaining 42915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 18529 35.43 - 70.86: 553 70.86 - 106.29: 89 106.29 - 141.73: 47 141.73 - 177.16: 21 Dihedral angle restraints: 19239 sinusoidal: 8259 harmonic: 10980 Sorted by residual: dihedral pdb=" CA MET F 116 " pdb=" C MET F 116 " pdb=" N TYR F 117 " pdb=" CA TYR F 117 " ideal model delta harmonic sigma weight residual 180.00 120.45 59.55 0 5.00e+00 4.00e-02 1.42e+02 dihedral pdb=" CA MET E 116 " pdb=" C MET E 116 " pdb=" N TYR E 117 " pdb=" CA TYR E 117 " ideal model delta harmonic sigma weight residual 180.00 120.51 59.49 0 5.00e+00 4.00e-02 1.42e+02 dihedral pdb=" CA VAL E 115 " pdb=" C VAL E 115 " pdb=" N MET E 116 " pdb=" CA MET E 116 " ideal model delta harmonic sigma weight residual 180.00 124.16 55.84 0 5.00e+00 4.00e-02 1.25e+02 ... (remaining 19236 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.112: 4672 1.112 - 2.224: 3 2.224 - 3.336: 3 3.336 - 4.448: 7 4.448 - 5.560: 17 Chirality restraints: 4702 Sorted by residual: chirality pdb=" C02 AJP A1106 " pdb=" C01 AJP A1106 " pdb=" C03 AJP A1106 " pdb=" C85 AJP A1106 " both_signs ideal model delta sigma weight residual False 2.60 -2.96 5.56 2.00e-01 2.50e+01 7.73e+02 chirality pdb=" C15 AJP A1106 " pdb=" C14 AJP A1106 " pdb=" C16 AJP A1106 " pdb=" C20 AJP A1106 " both_signs ideal model delta sigma weight residual False -2.42 3.14 -5.56 2.00e-01 2.50e+01 7.73e+02 chirality pdb=" C02 AJP C1106 " pdb=" C01 AJP C1106 " pdb=" C03 AJP C1106 " pdb=" C85 AJP C1106 " both_signs ideal model delta sigma weight residual False 2.60 -2.96 5.55 2.00e-01 2.50e+01 7.71e+02 ... (remaining 4699 not shown) Planarity restraints: 5286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET F 116 " -0.019 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" C MET F 116 " 0.066 2.00e-02 2.50e+03 pdb=" O MET F 116 " -0.024 2.00e-02 2.50e+03 pdb=" N TYR F 117 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET E 116 " 0.019 2.00e-02 2.50e+03 3.80e-02 1.45e+01 pdb=" C MET E 116 " -0.066 2.00e-02 2.50e+03 pdb=" O MET E 116 " 0.024 2.00e-02 2.50e+03 pdb=" N TYR E 117 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 193 " -0.019 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C ILE A 193 " 0.065 2.00e-02 2.50e+03 pdb=" O ILE A 193 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU A 194 " -0.022 2.00e-02 2.50e+03 ... (remaining 5283 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 2907 2.72 - 3.27: 29904 3.27 - 3.81: 49802 3.81 - 4.36: 61352 4.36 - 4.90: 102405 Nonbonded interactions: 246370 Sorted by model distance: nonbonded pdb=" O25 AJP A1106 " pdb=" O79 AJP A1106 " model vdw 2.176 2.432 nonbonded pdb=" O25 AJP C1106 " pdb=" O79 AJP C1106 " model vdw 2.176 2.432 nonbonded pdb=" O31 AJP C1106 " pdb=" O78 AJP C1106 " model vdw 2.179 2.432 nonbonded pdb=" OE2 GLU A 755 " pdb=" OG1 THR D 482 " model vdw 2.201 3.040 nonbonded pdb=" OH TYR B 128 " pdb=" OG SER B 243 " model vdw 2.223 3.040 ... (remaining 246365 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 1035 or resid 1101 through 1110)) selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.260 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 64.280 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.025 1.323 31823 Z= 1.239 Angle : 1.637 21.867 42940 Z= 0.878 Chirality : 0.360 5.560 4702 Planarity : 0.007 0.064 5286 Dihedral : 18.885 177.158 12189 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.69 % Allowed : 15.02 % Favored : 84.29 % Rotamer: Outliers : 0.80 % Allowed : 6.36 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 3.77 % Twisted General : 0.87 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.79 (0.10), residues: 3762 helix: -3.79 (0.07), residues: 1714 sheet: -4.40 (0.21), residues: 370 loop : -3.65 (0.12), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP C 861 HIS 0.012 0.003 HIS C 219 PHE 0.052 0.004 PHE E 99 TYR 0.027 0.004 TYR A 702 ARG 0.009 0.001 ARG B 485 Details of bonding type rmsd hydrogen bonds : bond 0.29930 ( 1093) hydrogen bonds : angle 10.37714 ( 3201) SS BOND : bond 0.02044 ( 10) SS BOND : angle 3.29454 ( 20) covalent geometry : bond 0.02539 (31813) covalent geometry : angle 1.63617 (42920) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 671 time to evaluate : 3.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.8004 (ptm) cc_final: 0.7786 (ptp) REVERT: A 635 SER cc_start: 0.9024 (t) cc_final: 0.8818 (p) REVERT: A 638 ASP cc_start: 0.8386 (m-30) cc_final: 0.7982 (m-30) REVERT: A 879 LYS cc_start: 0.8207 (ttpt) cc_final: 0.7829 (mmmt) REVERT: A 891 PHE cc_start: 0.8381 (m-10) cc_final: 0.7843 (m-10) REVERT: A 907 MET cc_start: 0.2736 (ppp) cc_final: 0.1586 (tpt) REVERT: A 922 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7697 (mm) REVERT: A 939 MET cc_start: 0.8371 (ttm) cc_final: 0.7791 (tpt) REVERT: A 966 PHE cc_start: 0.6804 (m-80) cc_final: 0.6580 (m-80) REVERT: B 36 PHE cc_start: 0.6833 (t80) cc_final: 0.6079 (t80) REVERT: B 127 TYR cc_start: 0.8158 (t80) cc_final: 0.7942 (t80) REVERT: B 392 GLN cc_start: 0.7477 (mp10) cc_final: 0.7158 (mp10) REVERT: B 490 ASP cc_start: 0.7680 (m-30) cc_final: 0.7386 (p0) REVERT: B 573 ILE cc_start: 0.8779 (tp) cc_final: 0.8562 (tp) REVERT: B 626 VAL cc_start: 0.9240 (t) cc_final: 0.8655 (m) REVERT: C 414 MET cc_start: 0.8112 (ptm) cc_final: 0.7815 (ptp) REVERT: C 627 GLU cc_start: 0.8037 (pp20) cc_final: 0.7805 (pp20) REVERT: C 816 TYR cc_start: 0.7858 (t80) cc_final: 0.7443 (t80) REVERT: C 863 TYR cc_start: 0.6058 (m-10) cc_final: 0.5583 (m-10) REVERT: C 891 PHE cc_start: 0.8310 (m-10) cc_final: 0.7936 (m-80) REVERT: C 907 MET cc_start: 0.2477 (ppp) cc_final: 0.1857 (tpt) REVERT: C 966 PHE cc_start: 0.6975 (m-80) cc_final: 0.6484 (m-80) REVERT: D 36 PHE cc_start: 0.6737 (t80) cc_final: 0.6405 (t80) REVERT: D 392 GLN cc_start: 0.7302 (mp10) cc_final: 0.6923 (mp10) REVERT: D 440 TYR cc_start: 0.8443 (p90) cc_final: 0.8221 (p90) REVERT: D 490 ASP cc_start: 0.7713 (m-30) cc_final: 0.7477 (p0) REVERT: E 67 LEU cc_start: 0.7897 (mt) cc_final: 0.7696 (mm) REVERT: E 88 TRP cc_start: 0.5912 (m100) cc_final: 0.5264 (t60) REVERT: F 88 TRP cc_start: 0.5698 (m100) cc_final: 0.5161 (t60) outliers start: 26 outliers final: 4 residues processed: 692 average time/residue: 0.4260 time to fit residues: 472.6299 Evaluate side-chains 379 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 374 time to evaluate : 3.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 115 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 319 optimal weight: 2.9990 chunk 286 optimal weight: 0.9980 chunk 158 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 193 optimal weight: 0.9980 chunk 153 optimal weight: 0.0980 chunk 296 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 220 optimal weight: 0.9990 chunk 343 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 60 ASN A 167 ASN A 202 ASN A 344 ASN A 575 ASN A 764 ASN A 950 HIS A 985 ASN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS B 60 ASN B 219 HIS B 224 ASN B 311 ASN B 318 ASN B 344 ASN B 350 ASN B 461 ASN B 508 GLN C 46 HIS C 60 ASN C 147 GLN C 167 ASN C 202 ASN C 344 ASN C 575 ASN C 764 ASN C 950 HIS C 985 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 HIS D 224 ASN D 311 ASN D 318 ASN ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 ASN D 461 ASN E 129 ASN F 129 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.143843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.107887 restraints weight = 54773.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.110298 restraints weight = 38605.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.110083 restraints weight = 38132.534| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31823 Z= 0.160 Angle : 0.971 31.883 42940 Z= 0.446 Chirality : 0.088 2.406 4702 Planarity : 0.005 0.058 5286 Dihedral : 19.474 179.975 5190 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.43 % Allowed : 11.35 % Favored : 88.22 % Rotamer: Outliers : 2.58 % Allowed : 11.00 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.49 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.12), residues: 3762 helix: -1.92 (0.11), residues: 1774 sheet: -4.05 (0.23), residues: 386 loop : -3.29 (0.14), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 766 HIS 0.005 0.001 HIS E 27 PHE 0.028 0.002 PHE C 517 TYR 0.031 0.002 TYR C1001 ARG 0.007 0.001 ARG D 692 Details of bonding type rmsd hydrogen bonds : bond 0.05016 ( 1093) hydrogen bonds : angle 5.30406 ( 3201) SS BOND : bond 0.00875 ( 10) SS BOND : angle 2.58606 ( 20) covalent geometry : bond 0.00345 (31813) covalent geometry : angle 0.96989 (42920) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 489 time to evaluate : 3.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8823 (pt) cc_final: 0.8592 (pt) REVERT: A 186 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8620 (pp) REVERT: A 302 GLN cc_start: 0.7568 (pm20) cc_final: 0.7347 (mp10) REVERT: A 414 MET cc_start: 0.7812 (ptm) cc_final: 0.7601 (ptp) REVERT: A 638 ASP cc_start: 0.8428 (m-30) cc_final: 0.8079 (m-30) REVERT: A 678 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7979 (mm-30) REVERT: A 879 LYS cc_start: 0.8240 (ttpt) cc_final: 0.7921 (mmmt) REVERT: A 891 PHE cc_start: 0.8481 (m-10) cc_final: 0.8104 (m-10) REVERT: A 901 PHE cc_start: 0.6798 (m-80) cc_final: 0.6408 (m-10) REVERT: A 939 MET cc_start: 0.7721 (ttm) cc_final: 0.7448 (tpt) REVERT: A 966 PHE cc_start: 0.6923 (m-80) cc_final: 0.6553 (m-80) REVERT: A 1005 TRP cc_start: 0.7158 (p-90) cc_final: 0.6896 (p-90) REVERT: B 46 HIS cc_start: 0.7375 (t-90) cc_final: 0.6996 (t-170) REVERT: B 114 ARG cc_start: 0.8504 (ttm170) cc_final: 0.8271 (ttm170) REVERT: B 133 PHE cc_start: 0.8803 (m-10) cc_final: 0.8394 (m-10) REVERT: B 357 THR cc_start: 0.7984 (p) cc_final: 0.7579 (t) REVERT: B 361 MET cc_start: 0.8226 (mtp) cc_final: 0.7881 (mtp) REVERT: B 392 GLN cc_start: 0.7664 (mp10) cc_final: 0.7300 (mp10) REVERT: B 408 MET cc_start: 0.6702 (mmm) cc_final: 0.6435 (mmm) REVERT: B 527 MET cc_start: 0.7661 (tpp) cc_final: 0.7366 (mmt) REVERT: B 573 ILE cc_start: 0.8700 (tp) cc_final: 0.8437 (tp) REVERT: C 50 LEU cc_start: 0.8688 (pt) cc_final: 0.8380 (pt) REVERT: C 302 GLN cc_start: 0.7576 (pm20) cc_final: 0.7271 (mp10) REVERT: C 412 HIS cc_start: 0.7378 (t-170) cc_final: 0.6722 (t70) REVERT: C 414 MET cc_start: 0.7834 (ptm) cc_final: 0.7567 (ptp) REVERT: C 627 GLU cc_start: 0.8221 (pp20) cc_final: 0.7752 (tm-30) REVERT: C 635 SER cc_start: 0.8977 (t) cc_final: 0.8721 (p) REVERT: C 816 TYR cc_start: 0.7793 (t80) cc_final: 0.7454 (t80) REVERT: C 863 TYR cc_start: 0.5939 (m-10) cc_final: 0.5322 (m-10) REVERT: C 891 PHE cc_start: 0.8324 (m-10) cc_final: 0.7983 (m-80) REVERT: C 907 MET cc_start: 0.2055 (ppp) cc_final: 0.1502 (tpt) REVERT: C 966 PHE cc_start: 0.7027 (m-80) cc_final: 0.6391 (m-80) REVERT: D 33 MET cc_start: 0.8757 (ptm) cc_final: 0.8509 (ptt) REVERT: D 269 GLU cc_start: 0.7605 (tp30) cc_final: 0.7048 (tp30) REVERT: D 357 THR cc_start: 0.7736 (p) cc_final: 0.7510 (t) REVERT: D 361 MET cc_start: 0.8163 (mtp) cc_final: 0.7782 (mtp) REVERT: D 373 TYR cc_start: 0.8891 (p90) cc_final: 0.8642 (p90) REVERT: D 392 GLN cc_start: 0.7470 (mp10) cc_final: 0.7053 (mp10) REVERT: D 408 MET cc_start: 0.7139 (mmm) cc_final: 0.5400 (mmm) REVERT: D 773 CYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7493 (m) REVERT: E 88 TRP cc_start: 0.6530 (m100) cc_final: 0.5475 (t60) REVERT: E 115 VAL cc_start: 0.6916 (OUTLIER) cc_final: 0.6481 (m) REVERT: E 116 MET cc_start: 0.1201 (tpp) cc_final: -0.0211 (pmm) REVERT: E 117 TYR cc_start: 0.1453 (m-80) cc_final: -0.1048 (m-80) REVERT: F 84 CYS cc_start: 0.8021 (m) cc_final: 0.7805 (m) REVERT: F 88 TRP cc_start: 0.6493 (m100) cc_final: 0.5485 (t60) REVERT: F 116 MET cc_start: 0.0739 (tpp) cc_final: 0.0213 (pmm) outliers start: 84 outliers final: 28 residues processed: 546 average time/residue: 0.3772 time to fit residues: 339.8134 Evaluate side-chains 414 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 383 time to evaluate : 3.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 167 ASN Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 143 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 57 optimal weight: 2.9990 chunk 127 optimal weight: 30.0000 chunk 129 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 290 optimal weight: 1.9990 chunk 279 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 233 optimal weight: 0.5980 chunk 236 optimal weight: 6.9990 chunk 373 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 167 ASN A 726 ASN B 24 GLN B 412 HIS C 112 GLN C 726 ASN C 985 ASN D 24 GLN D 112 GLN D 246 GLN D 412 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.142589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.106279 restraints weight = 54819.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.106303 restraints weight = 38287.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.106740 restraints weight = 41478.513| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 31823 Z= 0.158 Angle : 0.913 32.684 42940 Z= 0.414 Chirality : 0.083 2.265 4702 Planarity : 0.004 0.054 5286 Dihedral : 18.705 178.056 5187 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.40 % Allowed : 11.24 % Favored : 88.36 % Rotamer: Outliers : 2.86 % Allowed : 13.27 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.13), residues: 3762 helix: -1.06 (0.12), residues: 1780 sheet: -3.87 (0.24), residues: 352 loop : -3.07 (0.14), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 887 HIS 0.015 0.001 HIS E 27 PHE 0.026 0.002 PHE B 438 TYR 0.027 0.002 TYR C1001 ARG 0.006 0.000 ARG C 545 Details of bonding type rmsd hydrogen bonds : bond 0.04259 ( 1093) hydrogen bonds : angle 4.73758 ( 3201) SS BOND : bond 0.00521 ( 10) SS BOND : angle 2.54415 ( 20) covalent geometry : bond 0.00361 (31813) covalent geometry : angle 0.91196 (42920) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 410 time to evaluate : 3.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7568 (ptm160) REVERT: A 50 LEU cc_start: 0.8800 (pt) cc_final: 0.8554 (pt) REVERT: A 414 MET cc_start: 0.7845 (ptm) cc_final: 0.7630 (ptp) REVERT: A 638 ASP cc_start: 0.8346 (m-30) cc_final: 0.7923 (t0) REVERT: A 879 LYS cc_start: 0.8146 (ttpt) cc_final: 0.7875 (mmmt) REVERT: A 891 PHE cc_start: 0.8495 (m-10) cc_final: 0.8252 (m-80) REVERT: A 901 PHE cc_start: 0.6833 (m-80) cc_final: 0.6375 (m-10) REVERT: A 907 MET cc_start: 0.1825 (OUTLIER) cc_final: 0.1118 (tpt) REVERT: A 924 MET cc_start: 0.7423 (pmm) cc_final: 0.7140 (pmm) REVERT: A 939 MET cc_start: 0.7647 (ttm) cc_final: 0.7310 (tpt) REVERT: A 966 PHE cc_start: 0.6948 (m-80) cc_final: 0.6477 (m-80) REVERT: A 988 MET cc_start: 0.8253 (tmm) cc_final: 0.7648 (tmm) REVERT: A 1005 TRP cc_start: 0.7162 (p-90) cc_final: 0.6868 (p-90) REVERT: B 33 MET cc_start: 0.8674 (ptm) cc_final: 0.8376 (ptt) REVERT: B 189 GLU cc_start: 0.7305 (mm-30) cc_final: 0.7078 (mm-30) REVERT: B 357 THR cc_start: 0.7955 (p) cc_final: 0.7642 (t) REVERT: B 361 MET cc_start: 0.8254 (mtp) cc_final: 0.7939 (mtp) REVERT: B 392 GLN cc_start: 0.7735 (mp10) cc_final: 0.7354 (mp10) REVERT: B 438 PHE cc_start: 0.8535 (p90) cc_final: 0.8099 (p90) REVERT: B 527 MET cc_start: 0.7669 (tpp) cc_final: 0.7311 (mmt) REVERT: B 573 ILE cc_start: 0.8668 (tp) cc_final: 0.8413 (tp) REVERT: C 42 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7732 (ptm160) REVERT: C 50 LEU cc_start: 0.8632 (pt) cc_final: 0.8316 (pt) REVERT: C 414 MET cc_start: 0.7892 (ptm) cc_final: 0.7536 (ptp) REVERT: C 545 ARG cc_start: 0.7651 (ttm-80) cc_final: 0.7188 (ttm170) REVERT: C 585 MET cc_start: 0.8194 (mpt) cc_final: 0.7810 (mpt) REVERT: C 627 GLU cc_start: 0.8080 (pp20) cc_final: 0.7811 (tm-30) REVERT: C 635 SER cc_start: 0.9023 (t) cc_final: 0.8780 (p) REVERT: C 816 TYR cc_start: 0.7809 (t80) cc_final: 0.7498 (t80) REVERT: C 863 TYR cc_start: 0.5948 (m-10) cc_final: 0.5231 (m-10) REVERT: C 891 PHE cc_start: 0.8376 (m-10) cc_final: 0.8097 (m-80) REVERT: C 907 MET cc_start: 0.2179 (ppp) cc_final: 0.1429 (tpt) REVERT: C 924 MET cc_start: 0.7312 (ptp) cc_final: 0.6820 (mtm) REVERT: C 966 PHE cc_start: 0.7119 (m-80) cc_final: 0.6426 (m-80) REVERT: C 985 ASN cc_start: 0.7497 (OUTLIER) cc_final: 0.6935 (p0) REVERT: C 1002 LYS cc_start: 0.7214 (ttmp) cc_final: 0.6636 (mtmt) REVERT: C 1025 VAL cc_start: 0.8163 (t) cc_final: 0.7959 (p) REVERT: C 1029 MET cc_start: 0.7607 (mmt) cc_final: 0.7405 (tpp) REVERT: D 33 MET cc_start: 0.8631 (ptm) cc_final: 0.8383 (ptt) REVERT: D 189 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7348 (mm-30) REVERT: D 357 THR cc_start: 0.7735 (p) cc_final: 0.7532 (t) REVERT: D 361 MET cc_start: 0.8258 (mtp) cc_final: 0.7935 (mtp) REVERT: D 373 TYR cc_start: 0.8970 (p90) cc_final: 0.8706 (p90) REVERT: D 392 GLN cc_start: 0.7470 (mp10) cc_final: 0.7147 (mp10) REVERT: D 408 MET cc_start: 0.7069 (mmm) cc_final: 0.6145 (mmm) REVERT: D 527 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.6946 (mmt) REVERT: E 81 MET cc_start: 0.8687 (ttt) cc_final: 0.8476 (tmm) REVERT: E 88 TRP cc_start: 0.6581 (m100) cc_final: 0.5546 (t60) REVERT: E 115 VAL cc_start: 0.6782 (OUTLIER) cc_final: 0.6448 (m) REVERT: E 116 MET cc_start: 0.0811 (tpp) cc_final: 0.0257 (pmm) REVERT: E 122 ILE cc_start: 0.6976 (OUTLIER) cc_final: 0.6702 (mm) REVERT: F 88 TRP cc_start: 0.6552 (m100) cc_final: 0.5616 (t60) REVERT: F 116 MET cc_start: 0.0580 (tpp) cc_final: -0.0202 (pmm) outliers start: 93 outliers final: 44 residues processed: 477 average time/residue: 0.3843 time to fit residues: 303.7932 Evaluate side-chains 404 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 353 time to evaluate : 4.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 700 TYR Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 985 ASN Chi-restraints excluded: chain C residue 1015 LEU Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 589 CYS Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 143 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 180 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 106 optimal weight: 0.0020 chunk 227 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 323 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 173 optimal weight: 0.5980 chunk 351 optimal weight: 0.2980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.144537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.107803 restraints weight = 54580.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.108206 restraints weight = 35853.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.108555 restraints weight = 37271.146| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 31823 Z= 0.123 Angle : 0.878 32.638 42940 Z= 0.391 Chirality : 0.082 2.224 4702 Planarity : 0.004 0.053 5286 Dihedral : 18.140 178.730 5185 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.95 % Favored : 88.76 % Rotamer: Outliers : 2.46 % Allowed : 13.85 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.13), residues: 3762 helix: -0.56 (0.12), residues: 1778 sheet: -3.73 (0.23), residues: 380 loop : -2.92 (0.14), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 262 HIS 0.009 0.001 HIS F 107 PHE 0.019 0.001 PHE B 438 TYR 0.026 0.001 TYR C1001 ARG 0.006 0.000 ARG A 141 Details of bonding type rmsd hydrogen bonds : bond 0.03695 ( 1093) hydrogen bonds : angle 4.43767 ( 3201) SS BOND : bond 0.00197 ( 10) SS BOND : angle 1.62573 ( 20) covalent geometry : bond 0.00270 (31813) covalent geometry : angle 0.87745 (42920) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 420 time to evaluate : 3.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7586 (ptm160) REVERT: A 50 LEU cc_start: 0.8586 (pt) cc_final: 0.8340 (pt) REVERT: A 262 TRP cc_start: 0.8440 (t-100) cc_final: 0.8218 (t-100) REVERT: A 414 MET cc_start: 0.7849 (ptm) cc_final: 0.7621 (ptp) REVERT: A 642 GLN cc_start: 0.7454 (mp10) cc_final: 0.7206 (mp10) REVERT: A 879 LYS cc_start: 0.8120 (ttpt) cc_final: 0.7582 (mmmt) REVERT: A 891 PHE cc_start: 0.8474 (m-10) cc_final: 0.8194 (m-80) REVERT: A 907 MET cc_start: 0.1864 (OUTLIER) cc_final: 0.1055 (tpt) REVERT: A 939 MET cc_start: 0.7645 (ttm) cc_final: 0.7370 (tpt) REVERT: A 966 PHE cc_start: 0.6981 (m-80) cc_final: 0.6573 (m-80) REVERT: A 988 MET cc_start: 0.8237 (tmm) cc_final: 0.7510 (tmm) REVERT: A 1005 TRP cc_start: 0.7181 (p-90) cc_final: 0.6867 (p-90) REVERT: B 74 PHE cc_start: 0.8062 (t80) cc_final: 0.7816 (t80) REVERT: B 189 GLU cc_start: 0.7267 (mm-30) cc_final: 0.7026 (mm-30) REVERT: B 357 THR cc_start: 0.8036 (p) cc_final: 0.7700 (t) REVERT: B 361 MET cc_start: 0.8265 (mtp) cc_final: 0.7955 (mtp) REVERT: B 392 GLN cc_start: 0.7708 (mp10) cc_final: 0.7339 (mp10) REVERT: B 408 MET cc_start: 0.6686 (OUTLIER) cc_final: 0.5782 (mmt) REVERT: B 573 ILE cc_start: 0.8437 (tp) cc_final: 0.8177 (tp) REVERT: B 814 PHE cc_start: 0.7158 (t80) cc_final: 0.6929 (t80) REVERT: C 42 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7663 (ptm160) REVERT: C 262 TRP cc_start: 0.8353 (t-100) cc_final: 0.8148 (t-100) REVERT: C 414 MET cc_start: 0.7902 (ptm) cc_final: 0.7538 (ptp) REVERT: C 635 SER cc_start: 0.9011 (t) cc_final: 0.8780 (p) REVERT: C 816 TYR cc_start: 0.7775 (t80) cc_final: 0.7478 (t80) REVERT: C 863 TYR cc_start: 0.5960 (m-10) cc_final: 0.5289 (m-10) REVERT: C 891 PHE cc_start: 0.8374 (m-10) cc_final: 0.8086 (m-10) REVERT: C 907 MET cc_start: 0.2056 (ppp) cc_final: 0.1222 (tpt) REVERT: C 924 MET cc_start: 0.7225 (ptp) cc_final: 0.6743 (mtm) REVERT: C 966 PHE cc_start: 0.7069 (m-80) cc_final: 0.6405 (m-80) REVERT: C 985 ASN cc_start: 0.7547 (p0) cc_final: 0.6699 (p0) REVERT: C 1002 LYS cc_start: 0.7167 (ttmp) cc_final: 0.6611 (mtmt) REVERT: C 1009 PHE cc_start: 0.7326 (m-80) cc_final: 0.6960 (t80) REVERT: D 36 PHE cc_start: 0.7183 (t80) cc_final: 0.6694 (t80) REVERT: D 78 ASP cc_start: 0.7430 (p0) cc_final: 0.7069 (p0) REVERT: D 189 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7146 (mm-30) REVERT: D 357 THR cc_start: 0.7800 (p) cc_final: 0.7593 (t) REVERT: D 361 MET cc_start: 0.8274 (mtp) cc_final: 0.7913 (mtp) REVERT: D 408 MET cc_start: 0.6867 (mmm) cc_final: 0.6411 (mmp) REVERT: D 515 PHE cc_start: 0.8030 (OUTLIER) cc_final: 0.7664 (m-10) REVERT: D 527 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.6853 (mmt) REVERT: E 88 TRP cc_start: 0.6617 (m100) cc_final: 0.5570 (t60) REVERT: E 115 VAL cc_start: 0.6506 (OUTLIER) cc_final: 0.6161 (m) REVERT: E 116 MET cc_start: 0.0968 (tpp) cc_final: 0.0179 (pmm) REVERT: E 122 ILE cc_start: 0.6670 (OUTLIER) cc_final: 0.6359 (mm) REVERT: F 10 TYR cc_start: 0.8135 (m-80) cc_final: 0.7379 (m-10) REVERT: F 88 TRP cc_start: 0.6556 (m100) cc_final: 0.5583 (t60) REVERT: F 116 MET cc_start: 0.0483 (tpp) cc_final: -0.0287 (pmm) outliers start: 80 outliers final: 46 residues processed: 471 average time/residue: 0.4143 time to fit residues: 322.3144 Evaluate side-chains 413 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 359 time to evaluate : 3.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 700 TYR Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 1024 SER Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 589 CYS Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 143 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 28 optimal weight: 0.9990 chunk 230 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 275 optimal weight: 8.9990 chunk 276 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 354 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 371 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 282 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN B 112 GLN ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 ASN D 13 GLN D 246 GLN ** D 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.143439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.106458 restraints weight = 54482.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.106459 restraints weight = 36827.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.106891 restraints weight = 39139.642| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31823 Z= 0.143 Angle : 0.867 32.734 42940 Z= 0.384 Chirality : 0.081 2.193 4702 Planarity : 0.004 0.042 5286 Dihedral : 17.724 178.638 5184 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.87 % Favored : 88.86 % Rotamer: Outliers : 2.55 % Allowed : 15.11 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.14), residues: 3762 helix: -0.20 (0.12), residues: 1778 sheet: -3.60 (0.24), residues: 354 loop : -2.86 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 136 HIS 0.011 0.001 HIS B 412 PHE 0.033 0.001 PHE B 517 TYR 0.027 0.001 TYR C1001 ARG 0.006 0.000 ARG C 141 Details of bonding type rmsd hydrogen bonds : bond 0.03556 ( 1093) hydrogen bonds : angle 4.28336 ( 3201) SS BOND : bond 0.00236 ( 10) SS BOND : angle 1.47137 ( 20) covalent geometry : bond 0.00319 (31813) covalent geometry : angle 0.86632 (42920) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 378 time to evaluate : 3.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8549 (pt) cc_final: 0.8280 (pt) REVERT: A 408 MET cc_start: 0.7390 (tpp) cc_final: 0.7023 (mmm) REVERT: A 414 MET cc_start: 0.7852 (ptm) cc_final: 0.7600 (ptp) REVERT: A 642 GLN cc_start: 0.7478 (mp10) cc_final: 0.7130 (mp10) REVERT: A 891 PHE cc_start: 0.8460 (m-10) cc_final: 0.8191 (m-80) REVERT: A 966 PHE cc_start: 0.6987 (m-80) cc_final: 0.6594 (m-80) REVERT: A 988 MET cc_start: 0.8229 (tmm) cc_final: 0.7915 (tmm) REVERT: A 1005 TRP cc_start: 0.7134 (p-90) cc_final: 0.6833 (p-90) REVERT: B 189 GLU cc_start: 0.7219 (mm-30) cc_final: 0.7007 (mm-30) REVERT: B 357 THR cc_start: 0.7973 (p) cc_final: 0.7660 (t) REVERT: B 361 MET cc_start: 0.8260 (mtp) cc_final: 0.7954 (mtp) REVERT: B 392 GLN cc_start: 0.7691 (mp10) cc_final: 0.7350 (mp10) REVERT: B 573 ILE cc_start: 0.8384 (tp) cc_final: 0.8121 (tp) REVERT: B 814 PHE cc_start: 0.7214 (t80) cc_final: 0.6831 (t80) REVERT: C 50 LEU cc_start: 0.8445 (pt) cc_final: 0.8118 (pt) REVERT: C 414 MET cc_start: 0.7911 (ptm) cc_final: 0.7555 (ptp) REVERT: C 678 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7946 (mm-30) REVERT: C 721 MET cc_start: 0.7989 (ptt) cc_final: 0.7776 (ptt) REVERT: C 816 TYR cc_start: 0.7773 (t80) cc_final: 0.7316 (t80) REVERT: C 863 TYR cc_start: 0.5945 (m-10) cc_final: 0.5265 (m-10) REVERT: C 891 PHE cc_start: 0.8376 (m-10) cc_final: 0.8105 (m-10) REVERT: C 907 MET cc_start: 0.2089 (ppp) cc_final: 0.1204 (tpt) REVERT: C 966 PHE cc_start: 0.7066 (m-80) cc_final: 0.6457 (m-80) REVERT: C 1002 LYS cc_start: 0.7221 (ttmp) cc_final: 0.6659 (mtmt) REVERT: C 1009 PHE cc_start: 0.7412 (m-80) cc_final: 0.7065 (t80) REVERT: D 36 PHE cc_start: 0.7229 (t80) cc_final: 0.6752 (t80) REVERT: D 78 ASP cc_start: 0.7509 (p0) cc_final: 0.7255 (p0) REVERT: D 189 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7144 (mm-30) REVERT: D 361 MET cc_start: 0.8288 (mtp) cc_final: 0.7915 (mtp) REVERT: D 498 LEU cc_start: 0.9071 (pt) cc_final: 0.8774 (pt) REVERT: D 515 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.7880 (m-10) REVERT: D 527 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.6879 (mmt) REVERT: E 81 MET cc_start: 0.8655 (ttp) cc_final: 0.8160 (tmm) REVERT: E 88 TRP cc_start: 0.6596 (m100) cc_final: 0.5643 (t60) REVERT: E 115 VAL cc_start: 0.6398 (OUTLIER) cc_final: 0.6081 (m) REVERT: E 116 MET cc_start: 0.0940 (tpp) cc_final: 0.0125 (pmm) REVERT: E 122 ILE cc_start: 0.6688 (OUTLIER) cc_final: 0.6363 (mm) REVERT: F 88 TRP cc_start: 0.6525 (m100) cc_final: 0.5487 (t60) REVERT: F 115 VAL cc_start: 0.6493 (OUTLIER) cc_final: 0.6155 (m) REVERT: F 116 MET cc_start: 0.0623 (tpp) cc_final: -0.0302 (pmm) outliers start: 83 outliers final: 56 residues processed: 430 average time/residue: 0.3938 time to fit residues: 279.9334 Evaluate side-chains 395 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 334 time to evaluate : 3.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 700 TYR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 985 ASN Chi-restraints excluded: chain C residue 1015 LEU Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 589 CYS Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 11 MET Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 143 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 125 optimal weight: 1.9990 chunk 326 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 153 optimal weight: 0.4980 chunk 121 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 265 optimal weight: 7.9990 chunk 256 optimal weight: 10.0000 chunk 133 optimal weight: 6.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 HIS ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 HIS E 107 HIS F 107 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.140528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.104520 restraints weight = 54863.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.105507 restraints weight = 42155.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.106071 restraints weight = 40535.274| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 31823 Z= 0.237 Angle : 0.912 33.302 42940 Z= 0.409 Chirality : 0.083 2.209 4702 Planarity : 0.004 0.039 5286 Dihedral : 17.569 178.785 5184 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.86 % Favored : 87.85 % Rotamer: Outliers : 2.76 % Allowed : 16.03 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.14), residues: 3762 helix: -0.13 (0.13), residues: 1790 sheet: -3.62 (0.24), residues: 360 loop : -2.87 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 262 HIS 0.015 0.002 HIS B 46 PHE 0.027 0.002 PHE B 517 TYR 0.027 0.002 TYR C1001 ARG 0.007 0.000 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.03718 ( 1093) hydrogen bonds : angle 4.38717 ( 3201) SS BOND : bond 0.00380 ( 10) SS BOND : angle 1.67822 ( 20) covalent geometry : bond 0.00559 (31813) covalent geometry : angle 0.91160 (42920) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 353 time to evaluate : 3.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8697 (pt) cc_final: 0.8379 (pt) REVERT: A 414 MET cc_start: 0.7853 (ptm) cc_final: 0.7617 (ptp) REVERT: A 642 GLN cc_start: 0.7570 (mp10) cc_final: 0.7188 (mp10) REVERT: A 891 PHE cc_start: 0.8473 (m-10) cc_final: 0.8219 (m-80) REVERT: A 939 MET cc_start: 0.7533 (tpt) cc_final: 0.7059 (ttt) REVERT: A 966 PHE cc_start: 0.7059 (m-80) cc_final: 0.6395 (m-80) REVERT: A 988 MET cc_start: 0.8183 (tmm) cc_final: 0.7806 (tmm) REVERT: A 1005 TRP cc_start: 0.7205 (p-90) cc_final: 0.6976 (p-90) REVERT: B 41 PHE cc_start: 0.5089 (OUTLIER) cc_final: 0.3741 (p90) REVERT: B 189 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6898 (mm-30) REVERT: B 357 THR cc_start: 0.8047 (p) cc_final: 0.7697 (t) REVERT: B 361 MET cc_start: 0.8308 (mtp) cc_final: 0.8006 (mtp) REVERT: B 392 GLN cc_start: 0.7640 (mp10) cc_final: 0.7380 (mp10) REVERT: B 573 ILE cc_start: 0.8519 (tp) cc_final: 0.8252 (tp) REVERT: B 585 MET cc_start: 0.8936 (mmt) cc_final: 0.8056 (mmt) REVERT: B 814 PHE cc_start: 0.7238 (t80) cc_final: 0.6996 (t80) REVERT: C 50 LEU cc_start: 0.8605 (pt) cc_final: 0.8227 (pt) REVERT: C 414 MET cc_start: 0.7963 (ptm) cc_final: 0.7605 (ptp) REVERT: C 721 MET cc_start: 0.8095 (ptt) cc_final: 0.7868 (ptt) REVERT: C 816 TYR cc_start: 0.7762 (t80) cc_final: 0.7516 (t80) REVERT: C 863 TYR cc_start: 0.6127 (m-10) cc_final: 0.5565 (m-10) REVERT: C 891 PHE cc_start: 0.8435 (m-10) cc_final: 0.8191 (m-10) REVERT: C 907 MET cc_start: 0.2235 (ppp) cc_final: 0.1223 (tpt) REVERT: C 924 MET cc_start: 0.7682 (ptp) cc_final: 0.7151 (mtm) REVERT: C 966 PHE cc_start: 0.7018 (m-80) cc_final: 0.6478 (m-80) REVERT: C 985 ASN cc_start: 0.7971 (p0) cc_final: 0.7303 (p0) REVERT: C 1002 LYS cc_start: 0.7422 (ttmp) cc_final: 0.6837 (mtmt) REVERT: C 1009 PHE cc_start: 0.7408 (m-80) cc_final: 0.7157 (t80) REVERT: D 36 PHE cc_start: 0.7122 (t80) cc_final: 0.6653 (t80) REVERT: D 361 MET cc_start: 0.8333 (mtp) cc_final: 0.7938 (mtp) REVERT: D 515 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.8087 (m-10) REVERT: D 527 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.7039 (mmt) REVERT: E 88 TRP cc_start: 0.6584 (m100) cc_final: 0.5720 (t60) REVERT: E 115 VAL cc_start: 0.6266 (OUTLIER) cc_final: 0.6036 (m) REVERT: E 116 MET cc_start: 0.1068 (tpp) cc_final: 0.0314 (pmm) REVERT: E 122 ILE cc_start: 0.6574 (mp) cc_final: 0.6139 (mm) REVERT: F 88 TRP cc_start: 0.6452 (m100) cc_final: 0.5540 (t60) REVERT: F 115 VAL cc_start: 0.6294 (OUTLIER) cc_final: 0.6001 (m) REVERT: F 116 MET cc_start: 0.0486 (tpp) cc_final: -0.0477 (pmm) outliers start: 90 outliers final: 64 residues processed: 417 average time/residue: 0.3833 time to fit residues: 268.8575 Evaluate side-chains 401 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 332 time to evaluate : 3.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 700 TYR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 960 PHE Chi-restraints excluded: chain C residue 1015 LEU Chi-restraints excluded: chain C residue 1024 SER Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 589 CYS Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 17 CYS Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 151 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 121 optimal weight: 0.9980 chunk 237 optimal weight: 3.9990 chunk 253 optimal weight: 30.0000 chunk 352 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 179 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 281 optimal weight: 9.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 HIS C 985 ASN D 202 ASN ** D 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 HIS E 107 HIS F 107 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.140885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.104799 restraints weight = 54454.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.104970 restraints weight = 41841.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.105688 restraints weight = 41984.243| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 31823 Z= 0.197 Angle : 0.894 33.518 42940 Z= 0.398 Chirality : 0.082 2.222 4702 Planarity : 0.004 0.040 5286 Dihedral : 17.289 178.905 5184 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.59 % Favored : 88.12 % Rotamer: Outliers : 3.13 % Allowed : 16.43 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.14), residues: 3762 helix: 0.03 (0.13), residues: 1790 sheet: -3.57 (0.24), residues: 362 loop : -2.83 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 262 HIS 0.011 0.001 HIS F 107 PHE 0.029 0.002 PHE A 937 TYR 0.024 0.002 TYR C1001 ARG 0.004 0.000 ARG A 888 Details of bonding type rmsd hydrogen bonds : bond 0.03542 ( 1093) hydrogen bonds : angle 4.32993 ( 3201) SS BOND : bond 0.00613 ( 10) SS BOND : angle 1.78185 ( 20) covalent geometry : bond 0.00464 (31813) covalent geometry : angle 0.89304 (42920) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 359 time to evaluate : 3.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8617 (pt) cc_final: 0.8266 (pt) REVERT: A 414 MET cc_start: 0.7882 (ptm) cc_final: 0.7627 (ptp) REVERT: A 642 GLN cc_start: 0.7583 (mp10) cc_final: 0.7151 (mp10) REVERT: A 891 PHE cc_start: 0.8476 (m-10) cc_final: 0.8217 (m-80) REVERT: A 939 MET cc_start: 0.7502 (tpt) cc_final: 0.7006 (ttm) REVERT: A 966 PHE cc_start: 0.6964 (m-80) cc_final: 0.6346 (m-80) REVERT: A 988 MET cc_start: 0.8146 (tmm) cc_final: 0.7755 (tmm) REVERT: B 41 PHE cc_start: 0.5142 (OUTLIER) cc_final: 0.3756 (p90) REVERT: B 189 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6905 (mm-30) REVERT: B 357 THR cc_start: 0.7990 (p) cc_final: 0.7659 (t) REVERT: B 361 MET cc_start: 0.8332 (mtp) cc_final: 0.7777 (mtp) REVERT: B 515 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.7948 (m-10) REVERT: B 573 ILE cc_start: 0.8438 (tp) cc_final: 0.8168 (tp) REVERT: B 762 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9092 (tt) REVERT: B 814 PHE cc_start: 0.7294 (t80) cc_final: 0.6999 (t80) REVERT: C 50 LEU cc_start: 0.8585 (pt) cc_final: 0.8214 (pt) REVERT: C 414 MET cc_start: 0.7975 (ptm) cc_final: 0.7630 (ptp) REVERT: C 816 TYR cc_start: 0.7777 (t80) cc_final: 0.7502 (t80) REVERT: C 863 TYR cc_start: 0.6243 (m-10) cc_final: 0.5754 (m-10) REVERT: C 891 PHE cc_start: 0.8454 (m-10) cc_final: 0.8229 (m-10) REVERT: C 907 MET cc_start: 0.2148 (ppp) cc_final: 0.1210 (tpt) REVERT: C 966 PHE cc_start: 0.6935 (m-80) cc_final: 0.6488 (m-80) REVERT: C 1002 LYS cc_start: 0.7518 (ttmp) cc_final: 0.6971 (mtmt) REVERT: C 1009 PHE cc_start: 0.7410 (m-80) cc_final: 0.7180 (t80) REVERT: D 36 PHE cc_start: 0.7004 (t80) cc_final: 0.6522 (t80) REVERT: D 189 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7055 (mm-30) REVERT: D 361 MET cc_start: 0.8338 (mtp) cc_final: 0.7941 (mtp) REVERT: D 498 LEU cc_start: 0.9096 (pt) cc_final: 0.8758 (pt) REVERT: D 515 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.8157 (m-10) REVERT: D 527 MET cc_start: 0.7652 (OUTLIER) cc_final: 0.7207 (mmt) REVERT: E 81 MET cc_start: 0.8790 (ttp) cc_final: 0.8194 (tmm) REVERT: E 88 TRP cc_start: 0.6621 (m100) cc_final: 0.5801 (t60) REVERT: E 115 VAL cc_start: 0.5889 (OUTLIER) cc_final: 0.5673 (m) REVERT: E 116 MET cc_start: 0.0682 (tpp) cc_final: -0.0012 (pmm) REVERT: E 122 ILE cc_start: 0.6527 (OUTLIER) cc_final: 0.6108 (mm) REVERT: F 88 TRP cc_start: 0.6444 (m100) cc_final: 0.5613 (t60) REVERT: F 115 VAL cc_start: 0.6012 (OUTLIER) cc_final: 0.5736 (m) REVERT: F 116 MET cc_start: 0.0381 (tpp) cc_final: -0.0466 (pmm) outliers start: 102 outliers final: 66 residues processed: 433 average time/residue: 0.3680 time to fit residues: 269.1444 Evaluate side-chains 407 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 333 time to evaluate : 3.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 700 TYR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 960 PHE Chi-restraints excluded: chain C residue 985 ASN Chi-restraints excluded: chain C residue 1015 LEU Chi-restraints excluded: chain C residue 1024 SER Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 589 CYS Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 17 CYS Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 151 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 155 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 344 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 chunk 39 optimal weight: 0.7980 chunk 277 optimal weight: 7.9990 chunk 357 optimal weight: 9.9990 chunk 100 optimal weight: 0.1980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN A 412 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS F 107 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.143599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.108173 restraints weight = 54555.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.108827 restraints weight = 38056.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.109021 restraints weight = 40697.224| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31823 Z= 0.125 Angle : 0.868 33.219 42940 Z= 0.380 Chirality : 0.081 2.191 4702 Planarity : 0.003 0.037 5286 Dihedral : 16.991 178.737 5184 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.95 % Favored : 88.81 % Rotamer: Outliers : 2.30 % Allowed : 17.54 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.14), residues: 3762 helix: 0.26 (0.13), residues: 1794 sheet: -3.33 (0.25), residues: 380 loop : -2.76 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 262 HIS 0.012 0.001 HIS F 107 PHE 0.027 0.001 PHE A1009 TYR 0.024 0.001 TYR C 647 ARG 0.007 0.000 ARG A 888 Details of bonding type rmsd hydrogen bonds : bond 0.03299 ( 1093) hydrogen bonds : angle 4.19005 ( 3201) SS BOND : bond 0.00197 ( 10) SS BOND : angle 1.58238 ( 20) covalent geometry : bond 0.00283 (31813) covalent geometry : angle 0.86718 (42920) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 352 time to evaluate : 3.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8324 (pt) cc_final: 0.7999 (pt) REVERT: A 412 HIS cc_start: 0.7141 (t-170) cc_final: 0.6791 (t70) REVERT: A 414 MET cc_start: 0.7887 (ptm) cc_final: 0.7652 (ptp) REVERT: A 642 GLN cc_start: 0.7534 (mp10) cc_final: 0.7073 (mp10) REVERT: A 816 TYR cc_start: 0.7508 (t80) cc_final: 0.7081 (t80) REVERT: A 891 PHE cc_start: 0.8413 (m-10) cc_final: 0.8180 (m-10) REVERT: A 939 MET cc_start: 0.7533 (tpt) cc_final: 0.6926 (mtp) REVERT: A 966 PHE cc_start: 0.7054 (m-80) cc_final: 0.6379 (m-80) REVERT: A 988 MET cc_start: 0.8074 (tmm) cc_final: 0.7714 (tmm) REVERT: B 189 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6886 (mm-30) REVERT: B 357 THR cc_start: 0.7980 (p) cc_final: 0.7648 (t) REVERT: B 361 MET cc_start: 0.8275 (mtp) cc_final: 0.7730 (mtp) REVERT: B 515 PHE cc_start: 0.8074 (OUTLIER) cc_final: 0.7809 (m-10) REVERT: B 573 ILE cc_start: 0.8348 (tp) cc_final: 0.8077 (tp) REVERT: B 585 MET cc_start: 0.8744 (mmt) cc_final: 0.8270 (mmm) REVERT: B 762 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.9015 (tt) REVERT: B 814 PHE cc_start: 0.7276 (t80) cc_final: 0.6812 (t80) REVERT: C 50 LEU cc_start: 0.8289 (pt) cc_final: 0.7896 (pt) REVERT: C 414 MET cc_start: 0.7974 (ptm) cc_final: 0.7711 (ptp) REVERT: C 642 GLN cc_start: 0.7505 (mp10) cc_final: 0.7158 (mp10) REVERT: C 816 TYR cc_start: 0.7773 (t80) cc_final: 0.7396 (t80) REVERT: C 863 TYR cc_start: 0.6169 (m-10) cc_final: 0.5684 (m-10) REVERT: C 891 PHE cc_start: 0.8420 (m-10) cc_final: 0.8195 (m-10) REVERT: C 907 MET cc_start: 0.2045 (ppp) cc_final: 0.1131 (tpt) REVERT: C 924 MET cc_start: 0.7575 (ptp) cc_final: 0.7060 (mtm) REVERT: C 939 MET cc_start: 0.7424 (tpt) cc_final: 0.6923 (ttm) REVERT: C 966 PHE cc_start: 0.6985 (m-80) cc_final: 0.6427 (m-80) REVERT: C 985 ASN cc_start: 0.7702 (p0) cc_final: 0.7321 (p0) REVERT: C 1002 LYS cc_start: 0.7442 (ttmp) cc_final: 0.6905 (mtmt) REVERT: D 36 PHE cc_start: 0.7072 (t80) cc_final: 0.6597 (t80) REVERT: D 361 MET cc_start: 0.8274 (mtp) cc_final: 0.7877 (mtp) REVERT: D 498 LEU cc_start: 0.9055 (pt) cc_final: 0.8489 (pt) REVERT: D 515 PHE cc_start: 0.8319 (OUTLIER) cc_final: 0.8049 (m-10) REVERT: D 527 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.7103 (mmt) REVERT: E 81 MET cc_start: 0.8871 (ttp) cc_final: 0.8249 (tmm) REVERT: E 88 TRP cc_start: 0.6576 (m100) cc_final: 0.5885 (t60) REVERT: E 115 VAL cc_start: 0.5636 (OUTLIER) cc_final: 0.5306 (m) REVERT: E 116 MET cc_start: 0.0749 (tpp) cc_final: -0.0013 (pmm) REVERT: E 122 ILE cc_start: 0.6630 (OUTLIER) cc_final: 0.6221 (mm) REVERT: F 66 LYS cc_start: 0.7619 (mttt) cc_final: 0.7288 (mttm) REVERT: F 88 TRP cc_start: 0.6399 (m100) cc_final: 0.5585 (t60) REVERT: F 115 VAL cc_start: 0.5763 (OUTLIER) cc_final: 0.5428 (m) REVERT: F 116 MET cc_start: 0.0504 (tpp) cc_final: -0.0255 (pmm) outliers start: 75 outliers final: 54 residues processed: 407 average time/residue: 0.3742 time to fit residues: 258.2301 Evaluate side-chains 394 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 333 time to evaluate : 3.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 700 TYR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 960 PHE Chi-restraints excluded: chain C residue 1024 SER Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 589 CYS Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 75 HIS Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 151 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 330 optimal weight: 0.9980 chunk 268 optimal weight: 5.9990 chunk 127 optimal weight: 20.0000 chunk 320 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 313 optimal weight: 0.8980 chunk 287 optimal weight: 0.0050 chunk 348 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 247 optimal weight: 3.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS F 107 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.143631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.107273 restraints weight = 54470.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.108300 restraints weight = 38836.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.108757 restraints weight = 39016.434| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31823 Z= 0.125 Angle : 0.862 33.143 42940 Z= 0.376 Chirality : 0.081 2.175 4702 Planarity : 0.003 0.038 5286 Dihedral : 16.727 178.644 5184 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.85 % Favored : 88.92 % Rotamer: Outliers : 2.09 % Allowed : 17.97 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.14), residues: 3762 helix: 0.41 (0.13), residues: 1802 sheet: -3.27 (0.25), residues: 380 loop : -2.71 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 262 HIS 0.013 0.001 HIS E 107 PHE 0.034 0.001 PHE A 937 TYR 0.026 0.001 TYR D 732 ARG 0.015 0.000 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.03211 ( 1093) hydrogen bonds : angle 4.13407 ( 3201) SS BOND : bond 0.00198 ( 10) SS BOND : angle 1.52771 ( 20) covalent geometry : bond 0.00285 (31813) covalent geometry : angle 0.86139 (42920) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 341 time to evaluate : 3.320 Fit side-chains revert: symmetry clash REVERT: A 414 MET cc_start: 0.7891 (ptm) cc_final: 0.7516 (ptp) REVERT: A 642 GLN cc_start: 0.7502 (mp10) cc_final: 0.7297 (mp10) REVERT: A 816 TYR cc_start: 0.7446 (t80) cc_final: 0.6996 (t80) REVERT: A 891 PHE cc_start: 0.8443 (m-10) cc_final: 0.7907 (m-80) REVERT: A 939 MET cc_start: 0.7441 (tpt) cc_final: 0.6880 (mtp) REVERT: A 966 PHE cc_start: 0.7009 (m-80) cc_final: 0.6387 (m-80) REVERT: A 988 MET cc_start: 0.7991 (tmm) cc_final: 0.7735 (tmm) REVERT: B 41 PHE cc_start: 0.5131 (OUTLIER) cc_final: 0.3826 (p90) REVERT: B 189 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6850 (mm-30) REVERT: B 357 THR cc_start: 0.7971 (p) cc_final: 0.7642 (t) REVERT: B 361 MET cc_start: 0.8248 (mtp) cc_final: 0.7689 (mtp) REVERT: B 515 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.7815 (m-10) REVERT: B 573 ILE cc_start: 0.8338 (tp) cc_final: 0.8053 (tp) REVERT: B 585 MET cc_start: 0.8763 (mmt) cc_final: 0.8156 (mmt) REVERT: B 762 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8982 (tt) REVERT: B 814 PHE cc_start: 0.7261 (t80) cc_final: 0.6790 (t80) REVERT: C 414 MET cc_start: 0.7963 (ptm) cc_final: 0.7703 (ptp) REVERT: C 642 GLN cc_start: 0.7493 (mp10) cc_final: 0.7074 (mp10) REVERT: C 816 TYR cc_start: 0.7755 (t80) cc_final: 0.7375 (t80) REVERT: C 860 TYR cc_start: 0.7608 (m-80) cc_final: 0.7380 (m-80) REVERT: C 863 TYR cc_start: 0.6226 (m-10) cc_final: 0.5761 (m-10) REVERT: C 891 PHE cc_start: 0.8446 (m-10) cc_final: 0.8229 (m-10) REVERT: C 966 PHE cc_start: 0.6964 (m-80) cc_final: 0.6536 (m-80) REVERT: C 1002 LYS cc_start: 0.7461 (ttmp) cc_final: 0.6911 (mtmt) REVERT: D 36 PHE cc_start: 0.7089 (t80) cc_final: 0.6635 (t80) REVERT: D 189 GLU cc_start: 0.7045 (mm-30) cc_final: 0.6811 (mm-30) REVERT: D 361 MET cc_start: 0.8296 (mtp) cc_final: 0.7916 (mtp) REVERT: D 515 PHE cc_start: 0.8370 (OUTLIER) cc_final: 0.8098 (m-10) REVERT: D 527 MET cc_start: 0.7553 (OUTLIER) cc_final: 0.7113 (mmt) REVERT: E 81 MET cc_start: 0.8871 (ttp) cc_final: 0.8511 (tmm) REVERT: E 88 TRP cc_start: 0.6492 (m100) cc_final: 0.5806 (t60) REVERT: E 115 VAL cc_start: 0.5465 (OUTLIER) cc_final: 0.5157 (m) REVERT: E 116 MET cc_start: 0.0886 (tpp) cc_final: 0.0030 (pmm) REVERT: E 122 ILE cc_start: 0.6503 (OUTLIER) cc_final: 0.6064 (mm) REVERT: F 66 LYS cc_start: 0.7611 (mttt) cc_final: 0.7259 (mttm) REVERT: F 88 TRP cc_start: 0.6362 (m100) cc_final: 0.5579 (t60) REVERT: F 115 VAL cc_start: 0.5643 (OUTLIER) cc_final: 0.5267 (m) REVERT: F 116 MET cc_start: 0.0240 (tpp) cc_final: -0.0398 (pmm) REVERT: F 130 TYR cc_start: 0.4361 (m-80) cc_final: 0.4115 (m-80) outliers start: 68 outliers final: 53 residues processed: 389 average time/residue: 0.3712 time to fit residues: 246.0915 Evaluate side-chains 381 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 320 time to evaluate : 3.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 700 TYR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 960 PHE Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 960 PHE Chi-restraints excluded: chain C residue 1024 SER Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain D residue 589 CYS Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 151 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 125 optimal weight: 1.9990 chunk 29 optimal weight: 0.0770 chunk 38 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 265 optimal weight: 5.9990 chunk 64 optimal weight: 0.5980 chunk 203 optimal weight: 0.8980 chunk 191 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 363 optimal weight: 5.9990 chunk 137 optimal weight: 0.0770 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 GLN ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS F 107 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.144298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.108588 restraints weight = 54399.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.108124 restraints weight = 37270.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.108587 restraints weight = 40042.584| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 31823 Z= 0.122 Angle : 0.861 33.050 42940 Z= 0.374 Chirality : 0.081 2.166 4702 Planarity : 0.003 0.039 5286 Dihedral : 16.546 178.644 5184 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.77 % Favored : 89.02 % Rotamer: Outliers : 2.00 % Allowed : 18.37 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.14), residues: 3762 helix: 0.52 (0.13), residues: 1806 sheet: -3.03 (0.26), residues: 342 loop : -2.79 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 262 HIS 0.013 0.001 HIS E 107 PHE 0.035 0.001 PHE A 937 TYR 0.030 0.001 TYR D 732 ARG 0.006 0.000 ARG D 303 Details of bonding type rmsd hydrogen bonds : bond 0.03149 ( 1093) hydrogen bonds : angle 4.07144 ( 3201) SS BOND : bond 0.00185 ( 10) SS BOND : angle 1.45465 ( 20) covalent geometry : bond 0.00279 (31813) covalent geometry : angle 0.86056 (42920) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 339 time to evaluate : 3.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.7936 (ptm) cc_final: 0.7656 (ptp) REVERT: A 638 ASP cc_start: 0.8338 (m-30) cc_final: 0.7603 (t0) REVERT: A 642 GLN cc_start: 0.7474 (mp10) cc_final: 0.7156 (mp10) REVERT: A 719 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7275 (p0) REVERT: A 816 TYR cc_start: 0.7455 (t80) cc_final: 0.7186 (t80) REVERT: A 891 PHE cc_start: 0.8409 (m-10) cc_final: 0.7824 (m-10) REVERT: A 939 MET cc_start: 0.7500 (tpt) cc_final: 0.6884 (mtp) REVERT: A 966 PHE cc_start: 0.7015 (m-80) cc_final: 0.6404 (m-80) REVERT: A 988 MET cc_start: 0.7948 (tmm) cc_final: 0.7690 (tmm) REVERT: B 41 PHE cc_start: 0.5085 (OUTLIER) cc_final: 0.3804 (p90) REVERT: B 189 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6833 (mm-30) REVERT: B 357 THR cc_start: 0.7931 (p) cc_final: 0.7605 (t) REVERT: B 361 MET cc_start: 0.8280 (mtp) cc_final: 0.7729 (mtp) REVERT: B 425 CYS cc_start: 0.7138 (m) cc_final: 0.6866 (m) REVERT: B 515 PHE cc_start: 0.8116 (OUTLIER) cc_final: 0.7844 (m-10) REVERT: B 573 ILE cc_start: 0.8290 (tp) cc_final: 0.8011 (tp) REVERT: B 585 MET cc_start: 0.8772 (mmt) cc_final: 0.8385 (mmm) REVERT: B 762 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8969 (tt) REVERT: B 814 PHE cc_start: 0.7240 (t80) cc_final: 0.6776 (t80) REVERT: C 414 MET cc_start: 0.7977 (ptm) cc_final: 0.7718 (ptp) REVERT: C 816 TYR cc_start: 0.7741 (t80) cc_final: 0.7357 (t80) REVERT: C 860 TYR cc_start: 0.7687 (m-80) cc_final: 0.7430 (m-80) REVERT: C 863 TYR cc_start: 0.6241 (m-10) cc_final: 0.5762 (m-10) REVERT: C 891 PHE cc_start: 0.8405 (m-10) cc_final: 0.8175 (m-10) REVERT: C 907 MET cc_start: 0.1006 (ppp) cc_final: 0.0462 (tpt) REVERT: C 966 PHE cc_start: 0.7069 (m-80) cc_final: 0.6606 (m-80) REVERT: C 1002 LYS cc_start: 0.7464 (ttmp) cc_final: 0.6921 (mtmt) REVERT: D 36 PHE cc_start: 0.7120 (t80) cc_final: 0.6672 (t80) REVERT: D 189 GLU cc_start: 0.6965 (mm-30) cc_final: 0.6737 (mm-30) REVERT: D 361 MET cc_start: 0.8282 (mtp) cc_final: 0.7902 (mtp) REVERT: D 515 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.8058 (m-10) REVERT: D 527 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.7102 (mmt) REVERT: E 81 MET cc_start: 0.8890 (ttp) cc_final: 0.8472 (tmm) REVERT: E 88 TRP cc_start: 0.6521 (m100) cc_final: 0.5840 (t60) REVERT: E 115 VAL cc_start: 0.5058 (OUTLIER) cc_final: 0.4762 (m) REVERT: E 116 MET cc_start: 0.1028 (tpp) cc_final: -0.0055 (pmm) REVERT: E 122 ILE cc_start: 0.6415 (OUTLIER) cc_final: 0.5933 (mm) REVERT: E 130 TYR cc_start: 0.4446 (m-80) cc_final: 0.4207 (m-80) REVERT: F 66 LYS cc_start: 0.7560 (mttt) cc_final: 0.7190 (mttm) REVERT: F 88 TRP cc_start: 0.6333 (m100) cc_final: 0.5541 (t60) REVERT: F 115 VAL cc_start: 0.5469 (OUTLIER) cc_final: 0.5015 (m) REVERT: F 116 MET cc_start: 0.0650 (tpp) cc_final: -0.0328 (pmm) REVERT: F 130 TYR cc_start: 0.4515 (m-80) cc_final: 0.4277 (m-80) outliers start: 65 outliers final: 50 residues processed: 389 average time/residue: 0.3882 time to fit residues: 258.8478 Evaluate side-chains 383 residues out of total 3256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 324 time to evaluate : 3.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 700 TYR Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 642 GLN Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 960 PHE Chi-restraints excluded: chain C residue 1024 SER Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 589 CYS Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 17 CYS Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 151 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 334 optimal weight: 7.9990 chunk 230 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 330 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 360 optimal weight: 0.0020 chunk 139 optimal weight: 3.9990 chunk 262 optimal weight: 5.9990 chunk 286 optimal weight: 3.9990 chunk 329 optimal weight: 1.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 HIS B 337 GLN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 GLN ** D 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS F 101 HIS F 107 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.144291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.107868 restraints weight = 54259.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.107749 restraints weight = 38132.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.108579 restraints weight = 38141.710| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.207 31823 Z= 0.159 Angle : 0.945 59.199 42940 Z= 0.442 Chirality : 0.082 2.166 4702 Planarity : 0.003 0.039 5286 Dihedral : 16.544 178.643 5184 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.77 % Favored : 89.00 % Rotamer: Outliers : 2.12 % Allowed : 18.30 % Favored : 79.58 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.14), residues: 3762 helix: 0.54 (0.13), residues: 1806 sheet: -3.03 (0.26), residues: 342 loop : -2.78 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 262 HIS 0.014 0.001 HIS A 412 PHE 0.031 0.001 PHE A 937 TYR 0.057 0.001 TYR F 72 ARG 0.004 0.000 ARG D 303 Details of bonding type rmsd hydrogen bonds : bond 0.03158 ( 1093) hydrogen bonds : angle 4.07349 ( 3201) SS BOND : bond 0.00180 ( 10) SS BOND : angle 1.44760 ( 20) covalent geometry : bond 0.00357 (31813) covalent geometry : angle 0.94448 (42920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9939.04 seconds wall clock time: 176 minutes 4.31 seconds (10564.31 seconds total)